Modelling the brain

and The Swiss-based Ecole Polytechnique Fédérale de Lausanne (EPFL) are taking brain research to new heights.

Over the next two years, scientists from both organizations will work together using the computational capacity of IBM's eServer Blue Gene supercomputer to create a detailed model of the circuitry in the neocortex - the largest and most complex part of the human brain. Scientists hope to eventually build an accurate, computer-based model of the entire brain.

Relatively little is actually known about how the brain works. Using the digital model scientists will run computer-based simulations of the brain at the molecular level, shedding light on internal processes such as thought, perception and memory. Scientists also hope to understand more about how and why certain microcircuits in the brain malfunction - thought to be the cause of psychiatric disorders such as autism, schizophrenia and depression.

"Modelling the brain at the cellular level is a massive undertaking because of the hundreds of thousands of parameters that need to be taken into account," said Henry Markram, the EPFL professor heading up the project.

Markram is the founder of EPFL's Brain and Mind Institute, where more than 10 years of research and lab experiments have been consolidated into the world's most comprehensive set of empirical data on the micro-architecture of the neocortex.

Researchers from IBM will use their experience in simulating complex biological systems to help turn this data into a working 3-dimensional model re-creating the high-speed electro-chemical interactions of the brain's interior. Running on 4 racks of Blue Gene, the model will be capable of simulating brain processes in three dimensions with a precision never before achieved.

By using a Blue Gene supercomputer to run experiments in real time, Markram anticipates a substantial acceleration in the pace of brain research. "With an accurate computer-based model of the brain much of the pre-testing and planning normally required for a major experiment could be done 'in silico' rather than in the laboratory. With certain simulations we anticipate that a full day's worth of lab research could be done in a matter of seconds."

The system that will be installed at EPFL will occupy the floor space of about four refrigerators, and will have a peak processing speed of at least 22.8 trillion floating-point operations per second (22.8 teraflops), making it one of the most powerful supercomputers in the world.

The first phase of the project will be to make a software replica of a column of the neocortex. The neocortex constitutes about 85% of the human brain's total mass and is thought to be responsible for the cognitive functions of language, learning, memory and complex thought. An accurate replica of the neocortical column is the essential first step to simulating the whole brain and also will provide the link between genetic, molecular and cognitive levels of brain function. The second and subsequent phases will be to expand the simulation to include circuitry from other brain regions and eventually the whole brain.

The neocortex is organised into thousands of columns of neurons. Each column has a diameter of 0.5mm and contains 10,000 neurons. The neocortex is also organised into 6 layers and the golden neurons shown are the large output pyramidal neurons in the fifth layer. In the background are other neurons making up the neocortical column.

As part of the agreement with IBM, some of Blue Gene's time will also be allotted to other research projects. In one of the projects, researchers from IBM's Zurich Research Lab will work together with scientists from EPFL's Institutes of Complex Matter Physics and Nanostructure Physics to research future semiconductor (post-CMOS) technology.

Elsewhere at EPFL, researchers will use Blue Gene to look at the use of plasmas as a possible method of energy production. Another team will use Blue Gene to research the folding of proteins and their role in the development of Creutzfeldt-Jakob (mad cow) and other diseases.